Harmonized Landsat/Sentinel-2 Reflectance Products for Land Monitoring (Invited)

Many land applications require more frequent observations than can be obtained from a single 'Landsat class' sensor. Agricultural monitoring, inland water quality assessment, stand-scale phenology, and numerous other applications all require near-daily imagery at better than 1ha resolution. Thus the land science community has begun expressing a desire for a '30-meter MODIS' global monitoring capability. One cost-effective way to achieve this goal is via merging data from multiple, international observatories into a single virtual constellation. The Harmonized Landsat/Sentinel-2 (HLS) project has been working to generate a seamless surface reflectance product by combining observations from USGS/NASA Landsat-8 and ESA Sentinel-2. Harmonization in this context requires a series of radiometric and geometric transforms to create a single surface reflectance time series agnostic to sensor origin. Radiometric corrections include a common atmospheric correction using the Landsat-8 LaSRC/6S approach, a simple BRDF adjustment to constant solar and nadir view angle, and spectral bandpass adjustments to fit the Landsat-8 OLI reference. Data are then resampled to a consistent 30m UTM grid, using the Sentinel-2 global tile system. Cloud and shadow masking are also implemented. Quality assurance (QA) involves comparison of the output 30m HLS products with near-simultaneous MODIS nadir-adjusted observations. Prototoype HLS products have been processed for approximately 7% of the global land area using the NASA Earth Exchange (NEX) compute environment at NASA Ames, and can be downloaded from the HLS web site (https://hls.gsfc.nasa.gov). A wall-to-wall North America data set is being prepared for 2018. This talk will review the objectives and status of the HLS project, and illustrate applications of high-density optical time series data for agriculture and ecology. We also discuss lessons learned from HLS in the general context of implementing virtual constellations

Depictions of Thailand in Australian and Thai writings:Reflections of the Self and Other

This thesis offers both an examination of the depiction of Thailand in Australian novels, short stories and poems written in the 1980s and after, and an analysis of modern Thai novels and short stories that reflect similar themes to those covered in the Australian literature. One Australian film is also examined as the film provides an important framework for the analysis of some of the short stories and novels under consideration. The thesis establishes a dialogue between Thai and Australian literatures and demonstrates that the comparison of Australian representations of Thailand with Thai representations challenges constructively certain dominant political and social ideologies that enhance conservatism and the status quo in Thailand. The author acknowledges that the discussion of the representations of Thailand in contemporary Australian novels and short stories needs to take into account the colonial legacy and the discourse of Orientalism that tends to posit the ‘East’ as the ‘West’’s ‘Other’. Textual analysis is thus informed by post-colonial and cross-cultural theories, starting from Edward Said’s powerful and controversial critique of Western representation of the East in Orientalism. The first part of the thesis examines Australian crime stories and shows how certain Orientalist images and perceptions persist and help reinforce the image of the East and its people as the antithesis of the West. From Chapters Three through Six, however, more literary works by Australian authors are examined. The important finding is that most of the Australian authors under consideration attempt, though not always successfully, to resist and challenge the Eurocentric stereotypes of Asia and Asians that dominated Australian literature in earlier periods. This difference between contemporary Australian authors and their predecessors seems to reflect modern Australia’s endeavor to distinguish itself from the rest of the Western world and to redefine its relationship with Asia. As literary representations cannot be separated from socio-political contexts, the thesis also includes discussion of the Thai social and political history and, where appropriate, shows how colonialism and neo-colonialism exert their impact on modern Thailand

The role of dynamical polarization of the ligand to metal charge transfer excitations in {\em ab initio} determination of effective exchange parameters

The role of the bridging ligand on the effective Heisenberg coupling parameters is analyzed in detail. This analysis strongly suggests that the ligand-to-metal charge transfer excitations are responsible for a large part of the final value of the magnetic coupling constant. This permits to suggest a new variant of the Difference Dedicated Configuration Interaction (DDCI) method, presently one of the most accurate and reliable for the evaluation of magnetic effective interactions. This new method treats the bridging ligand orbitals mediating the interaction at the same level than the magnetic orbitals and preserves the high quality of the DDCI results while being much less computationally demanding. The numerical accuracy of the new approach is illustrated on various systems with one or two magnetic electrons per magnetic center. The fact that accurate results can be obtained using a rather reduced configuration interaction space opens the possibility to study more complex systems with many magnetic centers and/or many electrons per center.Comment: 7 pages, 4 figure

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

<p>Abstract</p> <p>Background</p> <p>In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models.</p> <p>Results</p> <p>The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence.</p> <p>Conclusions</p> <p>Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of interest, even when the latter display a high complexity (PROSITE signatures for example). In addition, these exact algorithms allow us to avoid the edge effect observed under the single sequence approximation, which leads to erroneous results, especially when the marginal distribution of the model displays a slow convergence toward the stationary distribution. We end up with a discussion on our method and on its potential improvements.</p

Total synthesis of Escherichia coli with a recoded genome

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Citation: Ekeberg, T., Svenda, M., Seibert, M. M., Abergel, C., Maia, F. R. N. C., Seltzer, V., . . . Hajdu, J. (2016). Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. Scientific Data, 3. doi:10.1038/sdata.2016.60Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms

RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions

BACKGROUND: Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-sequencing (RNA-seq) to detect sRNAs differentially expressed in Pseudomonas aeruginosa biofilm versus planktonic state. RESULTS: A computational algorithm was devised to detect and categorize sRNAs into 5 types: intergenic, intragenic, 5′-UTR, 3′-UTR, and antisense. Here we report a novel RsmY/RsmZ-type sRNA, termed RsmW, in P. aeruginosa up-transcribed in biofilm versus planktonic growth. RNA-Seq, 5’-RACE and Mfold predictions suggest RsmW has a secondary structure with 3 of 7 GGA motifs located on outer stem loops. Northern blot revealed two RsmW binding bands of 400 and 120 bases, suggesting RsmW is derived from the 3’-UTR of the upstream hypothetical gene, PA4570. RsmW expression is elevated in late stationary versus logarithmic growth phase in PB minimal media, at higher temperatures (37°C versus 28°C), and in both gacA and rhlR transposon mutants versus wild-type. RsmW specifically binds to RsmA protein in vitro and restores biofilm production and reduces swarming in an rsmY/rsmZ double mutant. PA4570 weakly resembles an RsmA/RsmN homolog having 49% and 51% similarity, and 16% and 17% identity to RsmA and RsmN amino acid sequences, respectively. PA4570 was unable to restore biofilm and swarming phenotypes in ΔrsmA deficient strains. CONCLUSION: Collectively, our study reveals an interesting theme regarding another sRNA regulator of the Rsm system and further unravels the complexities regulating adaptive responses for Pseudomonas species

Varieties of living things: Life at the intersection of lineage and metabolism

publication-status: Publishedtypes: Articl

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Contains fulltext : 95738.pdf (publisher's version ) (Open Access)BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm